Contacts of the strand formed by residues 339 - 344 (chain C) in PDB entry 1U7F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 339 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C PHE* 4.5 16.5 - - + +
305C ALA 3.1 16.8 - - - +
306C GLU* 3.6 21.5 + - + +
334C ILE* 3.9 4.0 - - - +
337C GLY 5.0 2.6 + - - -
338C CYS* 1.3 84.8 + - - +
340C LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C PHE* 3.3 8.0 - - - +
305C ALA 3.0 30.7 + - - +
315C VAL* 4.5 6.1 - - + -
320C CYS* 3.9 24.2 - - - -
323C ARG* 5.7 1.1 - - - +
332C CYS* 3.9 23.6 - - + -
334C ILE* 3.2 33.2 - - + +
339C ASN* 1.3 75.0 - - - +
341C LYS* 1.3 73.5 + - + +
342C ILE* 3.2 16.6 + - + +
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Residues in contact with LYS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C GLU* 2.8 44.4 - - + +
303C VAL 3.6 8.5 - - - +
304C PHE* 3.5 31.4 - - + -
320C CYS* 3.6 13.7 - - - -
323C ARG* 3.3 38.9 + - - +
340C LEU* 1.3 74.9 - - - +
342C ILE* 1.3 60.2 + - - +
343C PHE 3.5 7.6 - - - +
344C ASN* 4.9 0.2 - - - +
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C LEU* 4.7 10.1 - - + -
303C VAL* 2.8 47.3 + - + +
304C PHE* 4.1 2.7 - - - +
305C ALA* 3.8 30.3 - - + -
315C VAL* 3.7 30.1 - - + -
317C SER* 2.4 32.9 + - - +
320C CYS* 3.8 6.4 - - - +
323C ARG* 4.5 0.4 - - - -
340C LEU* 3.2 16.1 + - + +
341C LYS* 1.3 73.3 - - - +
343C PHE* 1.3 59.1 + - - +
372C ILE* 4.0 21.9 - - + +
374C MET* 5.2 2.7 - - - -
398C LEU* 4.7 4.9 - - + -
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Residues in contact with PHE 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C GLY 5.5 0.4 - - - -
302C GLU* 3.4 6.1 - - - +
303C VAL* 3.0 40.6 + - + +
319C ASN* 3.4 29.2 - - + -
323C ARG* 4.1 3.7 - - - +
341C LYS* 3.5 4.2 + - - +
342C ILE* 1.3 80.2 - - - +
344C ASN* 1.3 78.8 + - - +
345C ASN* 3.9 16.2 - - - -
348C PHE* 3.8 19.7 - + + -
369C MET 2.9 28.5 - - - -
372C ILE* 3.9 17.0 - - + -
400C LEU* 3.3 28.0 - - + -
403C PRO* 3.5 28.5 - - + -
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Residues in contact with ASN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C GLY 3.8 1.3 - - - -
302C GLU* 2.6 37.7 + - - +
319C ASN* 2.9 15.3 + - - +
323C ARG* 4.0 6.7 - - - +
343C PHE* 1.3 79.0 - - - +
345C ASN* 1.3 67.0 + - - +
346C GLN* 3.7 18.9 + - - +
347C GLU* 2.9 56.9 + - - +
348C PHE* 3.3 14.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il